rs13178541

chr5-135828929-A-Cchr5-135828929-A-Gchr5-135828929-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001349335.2(SLC25A48):c.-116-13487A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.711 in 152,094 control chromosomes in the GnomAD database, including 39,527 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.71 (39527 hom., cov: 33)
• Consequence: SLC25A48 NM_001349335.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.691

Genes affected

SLC25A48 (HGNC:30451): (solute carrier family 25 member 48) Predicted to enable acyl carnitine transmembrane transporter activity. Predicted to be involved in acyl carnitine transport and amino acid transport. Predicted to be located in mitochondrial inner membrane. Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.798 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC25A48	NM_001349335.2	c.-116-13487A>C		intron_variant
SLC25A48	NM_001349345.2	c.-116-13487A>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC25A48	ENST00000646290.1	c.-116-13487A>C		intron_variant

Frequencies

GnomAD3 genomes AF: 0.712 AC: 108136 AN: 151976 Hom.: 39503 Cov.: 33

Gnomad AFR AF: 0.541

Gnomad AMI AF: 0.893

Gnomad AMR AF: 0.678

Gnomad ASJ AF: 0.776

Gnomad EAS AF: 0.704

Gnomad SAS AF: 0.732

Gnomad FIN AF: 0.779

Gnomad MID AF: 0.829

Gnomad NFE AF: 0.804

Gnomad OTH AF: 0.748

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.711 AC: 108206 AN: 152094 Hom.: 39527 Cov.: 33 AF XY: 0.711 AC XY: 52841 AN XY: 74352

Gnomad4 AFR AF: 0.542

Gnomad4 AMR AF: 0.678

Gnomad4 ASJ AF: 0.776

Gnomad4 EAS AF: 0.704

Gnomad4 SAS AF: 0.732

Gnomad4 FIN AF: 0.779

Gnomad4 NFE AF: 0.804

Gnomad4 OTH AF: 0.748

Alfa AF: 0.687 Hom.: 2435

Bravo AF: 0.692

Asia WGS AF: 0.729 AC: 2537 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	6.2
Dann	Benign	0.66

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs13178541; hg19: chr5-135164618; COSMIC: COSV72644585; COSMIC: COSV72644585;